data_Y3O
# 
_chem_comp.id                                    Y3O 
_chem_comp.name                                  "(3P)-3-{4-[(2S,5R)-5-amino-2-methylpiperidin-1-yl]-6-chloro-7H-pyrrolo[2,3-d]pyrimidin-5-yl}benzonitrile" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H19 Cl N6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-03 
_chem_comp.pdbx_modified_date                    2023-03-31 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        366.847 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y3O 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8FKO 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
Y3O C1  C1  C  0 1 N N N 52.797 16.374 38.108 3.010  3.356  -1.235 C1  Y3O 1  
Y3O C4  C2  C  0 1 Y N N 52.074 13.924 35.404 1.018  2.420  1.758  C4  Y3O 2  
Y3O C5  C3  C  0 1 Y N N 52.165 15.124 36.089 1.722  3.176  0.842  C5  Y3O 3  
Y3O C3  C4  C  0 1 Y N N 52.632 12.773 35.936 0.863  1.061  1.566  C3  Y3O 4  
Y3O C7  C5  C  0 1 Y N N 53.378 14.015 37.859 2.127  1.199  -0.484 C7  Y3O 5  
Y3O C11 C6  C  0 1 Y N N 55.658 8.134  36.475 -1.890 -3.565 -0.521 C11 Y3O 6  
Y3O C6  C7  C  0 1 Y N N 52.812 15.168 37.325 2.281  2.571  -0.285 C6  Y3O 7  
Y3O C13 C8  C  0 1 Y N N 54.570 10.513 37.060 -0.006 -1.726 -0.035 C13 Y3O 8  
Y3O C8  C9  C  0 1 Y N N 53.283 12.810 37.170 1.417  0.443  0.444  C8  Y3O 9  
Y3O C9  C10 C  0 1 Y N N 53.870 11.576 37.761 1.250  -1.015 0.241  C9  Y3O 10 
Y3O C12 C11 C  0 1 Y N N 54.727 9.477  37.989 0.330  -3.086 -0.150 C12 Y3O 11 
Y3O C14 C12 C  0 1 Y N N 55.090 10.235 35.752 -1.346 -1.347 -0.190 C14 Y3O 12 
Y3O C10 C13 C  0 1 Y N N 53.696 11.135 39.040 2.227  -1.958 0.273  C10 Y3O 13 
Y3O C17 C14 C  0 1 N N N 55.797 13.081 32.586 -3.499 2.251  -0.266 C17 Y3O 14 
Y3O C16 C15 C  0 1 N N N 55.418 13.543 33.995 -2.362 2.028  -1.268 C16 Y3O 15 
Y3O C2  C16 C  0 1 N N N 55.408 10.706 33.353 -2.819 0.140  0.880  C2  Y3O 16 
Y3O C18 C17 C  0 1 N N R 55.136 11.744 32.264 -3.113 1.628  1.078  C18 Y3O 17 
Y3O C15 C18 C  0 1 N N S 55.788 12.506 35.057 -2.091 0.527  -1.398 C15 Y3O 18 
Y3O C19 C19 C  0 1 N N N 57.283 12.398 35.271 -3.349 -0.176 -1.912 C19 Y3O 19 
Y3O N1  N1  N  0 1 N N N 52.779 17.312 38.758 3.588  3.979  -1.988 N1  Y3O 20 
Y3O N4  N2  N  0 1 Y N N 55.262 8.274  37.745 -0.643 -3.963 -0.392 N4  Y3O 21 
Y3O N3  N3  N  0 1 Y N N 55.611 9.022  35.472 -2.247 -2.297 -0.425 N3  Y3O 22 
Y3O N2  N4  N  0 1 Y N N 54.205 9.902  39.180 1.683  -3.191 0.041  N2  Y3O 23 
Y3O N5  N5  N  0 1 N N N 55.178 11.202 34.720 -1.725 -0.021 -0.086 N5  Y3O 24 
Y3O N6  N6  N  0 1 N N N 55.631 11.236 30.951 -4.222 1.787  2.029  N6  Y3O 25 
Y3O CL1 CL1 CL 0 0 N N N 52.881 11.822 40.369 3.909  -1.645 0.565  CL1 Y3O 26 
Y3O H1  H1  H  0 1 N N N 51.566 13.885 34.452 0.591  2.891  2.631  H1  Y3O 27 
Y3O H2  H2  H  0 1 N N N 51.737 16.022 35.669 1.840  4.239  0.998  H2  Y3O 28 
Y3O H3  H3  H  0 1 N N N 52.563 11.842 35.393 0.311  0.475  2.286  H3  Y3O 29 
Y3O H4  H4  H  0 1 N N N 53.891 14.055 38.808 2.558  0.725  -1.354 H4  Y3O 30 
Y3O H5  H5  H  0 1 N N N 56.074 7.170  36.222 -2.652 -4.305 -0.717 H5  Y3O 31 
Y3O H6  H6  H  0 1 N N N 56.889 12.969 32.524 -3.667 3.320  -0.138 H6  Y3O 32 
Y3O H7  H7  H  0 1 N N N 55.464 13.834 31.857 -4.410 1.781  -0.638 H7  Y3O 33 
Y3O H8  H8  H  0 1 N N N 55.948 14.482 34.215 -2.649 2.431  -2.239 H8  Y3O 34 
Y3O H9  H9  H  0 1 N N N 54.332 13.717 34.032 -1.462 2.532  -0.915 H9  Y3O 35 
Y3O H10 H10 H  0 1 N N N 54.748 9.843  33.182 -2.530 -0.303 1.833  H10 Y3O 36 
Y3O H11 H11 H  0 1 N N N 56.457 10.386 33.272 -3.712 -0.360 0.504  H11 Y3O 37 
Y3O H12 H12 H  0 1 N N N 54.049 11.901 32.198 -2.225 2.126  1.468  H12 Y3O 38 
Y3O H13 H13 H  0 1 N N N 55.347 12.845 36.006 -1.272 0.366  -2.100 H13 Y3O 39 
Y3O H14 H14 H  0 1 N N N 57.490 11.641 36.042 -3.619 0.230  -2.886 H14 Y3O 40 
Y3O H15 H15 H  0 1 N N N 57.768 12.104 34.329 -3.155 -1.245 -2.004 H15 Y3O 41 
Y3O H16 H16 H  0 1 N N N 57.678 13.371 35.598 -4.167 -0.014 -1.210 H16 Y3O 42 
Y3O H17 H17 H  0 1 N N N 54.203 9.372  40.028 2.183  -4.022 0.015  H17 Y3O 43 
Y3O H18 H18 H  0 1 N N N 55.194 10.360 30.746 -4.437 2.763  2.174  H18 Y3O 44 
Y3O H19 H19 H  0 1 N N N 55.408 11.896 30.233 -5.037 1.279  1.721  H19 Y3O 45 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
Y3O N6  C18 SING N N 1  
Y3O C18 C17 SING N N 2  
Y3O C18 C2  SING N N 3  
Y3O C17 C16 SING N N 4  
Y3O C2  N5  SING N N 5  
Y3O C16 C15 SING N N 6  
Y3O N5  C15 SING N N 7  
Y3O N5  C14 SING N N 8  
Y3O C15 C19 SING N N 9  
Y3O C4  C3  DOUB Y N 10 
Y3O C4  C5  SING Y N 11 
Y3O N3  C14 DOUB Y N 12 
Y3O N3  C11 SING Y N 13 
Y3O C14 C13 SING Y N 14 
Y3O C3  C8  SING Y N 15 
Y3O C5  C6  DOUB Y N 16 
Y3O C11 N4  DOUB Y N 17 
Y3O C13 C9  SING Y N 18 
Y3O C13 C12 DOUB Y N 19 
Y3O C8  C9  SING N N 20 
Y3O C8  C7  DOUB Y N 21 
Y3O C6  C7  SING Y N 22 
Y3O C6  C1  SING N N 23 
Y3O N4  C12 SING Y N 24 
Y3O C9  C10 DOUB Y N 25 
Y3O C12 N2  SING Y N 26 
Y3O C1  N1  TRIP N N 27 
Y3O C10 N2  SING Y N 28 
Y3O C10 CL1 SING N N 29 
Y3O C4  H1  SING N N 30 
Y3O C5  H2  SING N N 31 
Y3O C3  H3  SING N N 32 
Y3O C7  H4  SING N N 33 
Y3O C11 H5  SING N N 34 
Y3O C17 H6  SING N N 35 
Y3O C17 H7  SING N N 36 
Y3O C16 H8  SING N N 37 
Y3O C16 H9  SING N N 38 
Y3O C2  H10 SING N N 39 
Y3O C2  H11 SING N N 40 
Y3O C18 H12 SING N N 41 
Y3O C15 H13 SING N N 42 
Y3O C19 H14 SING N N 43 
Y3O C19 H15 SING N N 44 
Y3O C19 H16 SING N N 45 
Y3O N2  H17 SING N N 46 
Y3O N6  H18 SING N N 47 
Y3O N6  H19 SING N N 48 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
Y3O SMILES           ACDLabs              12.01 "N#Cc1cccc(c1)c1c2c(ncnc2[NH]c1Cl)N1CC(N)CCC1C"                                                                                                                     
Y3O InChI            InChI                1.06  "InChI=1S/C19H19ClN6/c1-11-5-6-14(22)9-26(11)19-16-15(13-4-2-3-12(7-13)8-21)17(20)25-18(16)23-10-24-19/h2-4,7,10-11,14H,5-6,9,22H2,1H3,(H,23,24,25)/t11-,14+/m0/s1" 
Y3O InChIKey         InChI                1.06  IWFMUUASEIUTAN-SMDDNHRTSA-N                                                                                                                                         
Y3O SMILES_CANONICAL CACTVS               3.385 "C[C@H]1CC[C@@H](N)CN1c2ncnc3[nH]c(Cl)c(c4cccc(c4)C#N)c23"                                                                                                          
Y3O SMILES           CACTVS               3.385 "C[CH]1CC[CH](N)CN1c2ncnc3[nH]c(Cl)c(c4cccc(c4)C#N)c23"                                                                                                             
Y3O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]1CC[C@H](CN1c2c3c(c([nH]c3ncn2)Cl)c4cccc(c4)C#N)N"                                                                                                           
Y3O SMILES           "OpenEye OEToolkits" 2.0.7 "CC1CCC(CN1c2c3c(c([nH]c3ncn2)Cl)c4cccc(c4)C#N)N"                                                                                                                   
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
Y3O "SYSTEMATIC NAME" ACDLabs              12.01 "(3P)-3-{4-[(2S,5R)-5-amino-2-methylpiperidin-1-yl]-6-chloro-7H-pyrrolo[2,3-d]pyrimidin-5-yl}benzonitrile"                 
Y3O "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-[4-[(2~{S},5~{R})-5-azanyl-2-methyl-piperidin-1-yl]-6-chloranyl-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]benzenecarbonitrile" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y3O "Create component" 2023-01-03 RCSB 
Y3O "Initial release"  2023-04-05 RCSB 
# 
